For details on the H statistic see
Fay and Wu 2000.
Any questions or difficulties contact me at jfay(a)genetics.wustl.edu

Enter the sample size:
[2:5000]

Enter the recombination rate: [0:100]

Here, the size of the region and 4Nc is for 1kb. So to get 4Nc/bp = 0.001 enter 1 above.

Enter the number of simulations: [1:100000]

Enter the probability of back-mutation: [0:0.5]

Generally, the rate of divergence at synonymous sites divided by 3 is the probability of a back-mutation (see paper for details). Divergence between D. melanogaster and D. simulans is typically between 0.05 - 0.10, and divergence between humans and chimpanzees is typically between 0.007 - 0.012.

Enter the frequencies of segregating sites of various types:

Example: f1=3 f2=2 f3=1 f8=1 f9=1; where, for example, f1=2 means that the number of mutations of size 1 (externalmutations) is 2.

The results of the H-statistic are now scaled by the variance of the statistic. For more information see Zeng, Shi, Fu and Wu PDF